Drought Stress Responses in Context-Specific Genome-Scale Metabolic Models of <i>Arabidopsis thaliana</i>
Drought perturbs metabolism in plants and limits their growth. Because drought stress on crops affects their yields, understanding the complex adaptation mechanisms evolved by plants against drought will facilitate the development of drought-tolerant crops for agricultural use. In this study, we exa...
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-04-01
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| Series: | Metabolites |
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| Online Access: | https://www.mdpi.com/2218-1989/10/4/159 |
| _version_ | 1827718374408323072 |
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| author | Ratklao Siriwach Fumio Matsuda Kentaro Yano Masami Yokota Hirai |
| author_facet | Ratklao Siriwach Fumio Matsuda Kentaro Yano Masami Yokota Hirai |
| author_sort | Ratklao Siriwach |
| collection | DOAJ |
| description | Drought perturbs metabolism in plants and limits their growth. Because drought stress on crops affects their yields, understanding the complex adaptation mechanisms evolved by plants against drought will facilitate the development of drought-tolerant crops for agricultural use. In this study, we examined the metabolic pathways of <i>Arabidopsis thaliana</i> which respond to drought stress by omics-based in silico analyses. We proposed an analysis pipeline to understand metabolism under specific conditions based on a genome-scale metabolic model (GEM). Context-specific GEMs under drought and well-watered control conditions were reconstructed using transcriptome data and examined using metabolome data. The metabolic fluxes throughout the metabolic network were estimated by flux balance analysis using the context-specific GEMs. We used in silico methods to identify an important reaction contributing to biomass production and clarified metabolic reaction responses under drought stress by comparative analysis between drought and control conditions. This proposed pipeline can be applied in other studies to understand metabolic changes under specific conditions using <i>Arabidopsis</i> GEM or other available plant GEMs. |
| first_indexed | 2024-03-10T20:23:14Z |
| format | Article |
| id | doaj.art-6f8b0078c6ad41b5b63cb7e7e0ea55e0 |
| institution | Directory Open Access Journal |
| issn | 2218-1989 |
| language | English |
| last_indexed | 2024-03-10T20:23:14Z |
| publishDate | 2020-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Metabolites |
| spelling | doaj.art-6f8b0078c6ad41b5b63cb7e7e0ea55e02023-11-19T22:02:41ZengMDPI AGMetabolites2218-19892020-04-0110415910.3390/metabo10040159Drought Stress Responses in Context-Specific Genome-Scale Metabolic Models of <i>Arabidopsis thaliana</i>Ratklao Siriwach0Fumio Matsuda1Kentaro Yano2Masami Yokota Hirai3RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, JapanDepartment of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka 565-0871, JapanBioinformatics Laboratory, Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, JapanRIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, JapanDrought perturbs metabolism in plants and limits their growth. Because drought stress on crops affects their yields, understanding the complex adaptation mechanisms evolved by plants against drought will facilitate the development of drought-tolerant crops for agricultural use. In this study, we examined the metabolic pathways of <i>Arabidopsis thaliana</i> which respond to drought stress by omics-based in silico analyses. We proposed an analysis pipeline to understand metabolism under specific conditions based on a genome-scale metabolic model (GEM). Context-specific GEMs under drought and well-watered control conditions were reconstructed using transcriptome data and examined using metabolome data. The metabolic fluxes throughout the metabolic network were estimated by flux balance analysis using the context-specific GEMs. We used in silico methods to identify an important reaction contributing to biomass production and clarified metabolic reaction responses under drought stress by comparative analysis between drought and control conditions. This proposed pipeline can be applied in other studies to understand metabolic changes under specific conditions using <i>Arabidopsis</i> GEM or other available plant GEMs.https://www.mdpi.com/2218-1989/10/4/159<i>Arabidopsis</i>droughtflux balance analysisgenome-scale metabolic modelmetabolismmetabolome |
| spellingShingle | Ratklao Siriwach Fumio Matsuda Kentaro Yano Masami Yokota Hirai Drought Stress Responses in Context-Specific Genome-Scale Metabolic Models of <i>Arabidopsis thaliana</i> Metabolites <i>Arabidopsis</i> drought flux balance analysis genome-scale metabolic model metabolism metabolome |
| title | Drought Stress Responses in Context-Specific Genome-Scale Metabolic Models of <i>Arabidopsis thaliana</i> |
| title_full | Drought Stress Responses in Context-Specific Genome-Scale Metabolic Models of <i>Arabidopsis thaliana</i> |
| title_fullStr | Drought Stress Responses in Context-Specific Genome-Scale Metabolic Models of <i>Arabidopsis thaliana</i> |
| title_full_unstemmed | Drought Stress Responses in Context-Specific Genome-Scale Metabolic Models of <i>Arabidopsis thaliana</i> |
| title_short | Drought Stress Responses in Context-Specific Genome-Scale Metabolic Models of <i>Arabidopsis thaliana</i> |
| title_sort | drought stress responses in context specific genome scale metabolic models of i arabidopsis thaliana i |
| topic | <i>Arabidopsis</i> drought flux balance analysis genome-scale metabolic model metabolism metabolome |
| url | https://www.mdpi.com/2218-1989/10/4/159 |
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